cell_attributes

#cell attributes like area, mcherry intensity, etc at t=0

#cells with pup1-rfp
modc_cells.pup1.1 <- read_csv("~/plots/pup1-rfp-gfp-decay/5-5-20-20mGFP/data/5-5-21-20mGFP_mODC_attributes_puncta_20min.csv") %>% 
  rename( "gfp.mean.bg.af.sub.new" ="gfp.mean.bg.sub.new") %>% 
  filter(experiment == "20min")


modc_cells.pup1.2 <- read_csv("~/plots/pup1-rfp-gfp-decay/6-28-22-modc-gfp/data/6-28-22_mODC_pup1_attributes.csv") %>% 
  filter(experiment == "20min")


cln2_cells.pup1.1 <- read_csv("~/plots/pup1-rfp-gfp-decay/5-9-21-30mGFP/data/5-9-21-30mGFP_cln2_puncta_attributes.csv") %>% 
   rename( "gfp.mean.bg.af.sub.new" ="gfp.mean.bg.sub.new") %>% 
  filter(experiment == "20min")

cln2_cells.pup1.2 <- read_csv("~/plots/pup1-rfp-gfp-decay/6-28-22-cln2-gfp/data/6-28-22_cln2_pup1_attributes.csv")
cln2_cells.pup1.3 <- read_csv("~/plots/pup1-rfp-gfp-decay/7-20-22-cln2-gfp/data/7-20-22_cln2_pup1_attributes.csv")
#10-18-22 Repeate
cln2_cells.pup1.4 <- read_csv("~/plots/pup1-rfp-gfp-decay/10-7-22-cln2-gfp/data/10-7-22_cln2_pup1_attributes.csv")


stable_cells.pup1 <- read_csv("~/plots/pup1-rfp-gfp-decay/4-28-21-8hrGFP/data/4-28-21-8hrGFP_attributes.csv") %>% 
  rename("gfp.mean.bg.af.sub.new" = "gfp.mean.bg.sub.new" )

stable_cells.pup2 <- read_csv("~/plots/pup1-rfp-gfp-decay/7-20-22-stable-gfp/data/7-20-22_stable_pup1_attributes.csv")
#10-7-22 repeate
stable_cells.pup3 <- read_csv("~/plots/pup1-rfp-gfp-decay/10-7-22-stable-gfp/data/10-7-22_stable_pup1_attributes.csv")


all.pup1.data <- bind_rows(cln2_cells.pup1.4 %>% 
                             mutate(degron = "cln2.4"),
                           stable_cells.pup3 %>% 
                             mutate(degron = "stable.3")) %>% 
  # bind_rows(modc_cells.pup1.1 %>% 
  #           mutate(degron = "mODC"),
  #           modc_cells.pup1.2 %>% 
  #             mutate(degron = "mODC.2"),
  #         cln2_cells.pup1.1 %>% 
  #          mutate(degron = "cln2"),
  #         cln2_cells.pup1.2 %>% 
  #           mutate(degron = "cln2.2"),
  #          cln2_cells.pup1.3 %>% 
  #           mutate(degron = "cln2.3"),
  #         stable_cells.pup1 %>% 
  #           mutate(degron = "stable"),
  #         stable_cells.pup2 %>% 
  #           mutate(degron = "stable.2")) %>% 
  select(unique.trackID, 
         gfp.mean.bg.af.sub.new, 
         gfp.sum.bg.af.sub,
         area, 
         area.puncta,
         # BB_B,
         # BB_C,
         Elip_B,
         Elip_C,
         no.of.voxels,
         pos.x,
         pos.y,
         spheracity,
         volume,
         rfp.mean.bg.sub,
         rfp.sum.bg.sub,
         dapi.mean.bg.sub,
         dapi.sum.bg.sub,
         rfp.mean.bg.sub.puncta,
         # rfp.mean.af.sub.puncta,
         rfp.sum.bg.sub.puncta,
         # rfp.sum.af.sub.puncta,
         dapi.sum.bg.sub.puncta,
         # dapi.sum.af.sub.puncta,
         dapi.mean.bg.sub.puncta,
         # dapi.mean.af.sub.puncta,
         degron,area.puncta) %>% 
  rename("cell.id"="unique.trackID" ) %>% 
  mutate(red = "pup1-rfp",
         treatment = "none",
         cell.id = paste0(cell.id ,"_",degron,"_",red,"_",treatment))

# all.pup1.data %>% 
#   write_csv(.,"~/plots/all_data/all_pup1_cell_attr.csv")

#10-18-22 
read_csv("~/plots/all_data/all_pup1_cell_attr.csv") %>% 
  bind_rows(.,all.pup1.data) %>% 
  write_csv(.,path = "~/plots/all_data/all_pup1_cell_attr.csv")

#old tef2-mcherry values

#repeate of the tef2-mcherry experiments

read_csv("~/plots/tef2-mch/8-4-22-calcufluor/mODC-tef2/8-4-22_modc_tef2-mch_attributes.csv")

Rows: 2504 Columns: 56
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr  (5): unique.trackID, experiment, field, exp.field, sample
dbl (51): gfp.mean.bg.af.sub.new, gfp.mean.bg.sub, gfp.sum.bg.sub, avg.gfp.bg, area, pos.x, pos.y, timepoint, trac...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

#combining the old tef2-mch experiment data with the repeated experiments

tef2.mch.all.select %>% 
  write_csv(.,"~/plots/all_data/all_tef2-mch_attr.csv")

##MG135 proteasome inhibition experiments

1uM

cell.info.1uM <- read.csv("~/plots/proteasome_inhibition/data/4-1-22/1uM/4-1-22-GFP_mODC_1uMMG132_attributes.csv")

2.5uM

cell.info.2.5uM <- read.csv("~/plots/proteasome_inhibition/data/4-1-22/2.5uM/4-1-22-GFP_mODC_2.5uMMG132_attributes.csv")

5uM

cell.info.5uM <- read.csv("~/plots/proteasome_inhibition/data/4-1-22/5uM/4-1-22-GFP_mODC_5uMMG132_attributes.csv")

50uM

cell.info.50uM <- read.csv("~/plots/proteasome_inhibition/data/2-3-22/MG132_50uM/2-3-22-GFP_mODC_50uMMG132_attributes.csv")

Combined dataframes

all.Prot.Inhi.info %>% 
  write_csv(.,"~/plots/all_data/all_mg135_attr.csv")